fern.tools

Class NumberTools

java.lang.Object

fern.tools.NumberTools

public class NumberTools
extends Object

Contains some common methods to handle number related data structures.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
NumberTools()

Method Summary

Modifier and Type	Method and Description
static int	argMax(Map<Integer,Integer> l) Gets the argmax of the given map.
static double	avg(double[] a) Gets the avg of the array
static double	calculateHistogramDistance(Map<Integer,Integer> h1, Map<Integer,Integer> h2) Calculates the histogram distance of two histograms.
static double[]	convertIntToDouble(int[] a) Performs a deep cast of an int[].
static double[][]	createHistogram(Collection<double[]> data, int numBins, int... indices) Creates a histogram from the given data.
static int[]	createHistogram(int[] a) Create a histogram for the given array.
static Map<Integer,Integer>	createHistogramAsMap(int[] a) Create a histogram map for the given array.
static int[]	createInverse(int[] a) Creates the inverse array to the given array.
static Map<Integer,Integer>	createInverseAsMap(int[] a) Creates the inverse map to the given array.
static void	cumSum(int[] l) Replaces the values in the given array with the cumulative sum of the array.
static int	faculty(int i) Gets the faculty
static int[]	getContentAsArray(cern.colt.bitvector.BitVector bv) Gets the indices of the set bits of the given BitVector as array.
static cern.colt.bitvector.BitVector	getContentAsBitVector(int[] a) Gets the content of the given array as BitVector, which means, that the BitVector will have a size equal to the maximal value in the array and contains a 1 for each element which is contained at least once in the array
static String	getHistogramAsString(Map<Integer,Integer> h) Gets a string representation of the histogram map.
static int[]	getNumbersTo(int n) Gets the numbers from 0 to n in an array.
static double[]	interpolateLinear(double interval, double[] time, double[] value) Performs a linear interpolation of the values.
static double	interpolateLinear(double desiredTime, double beforeTime, double afterTime, double beforeValue, double afterValue) Interpolates a value
static String[]	inverse(String[] a) Inverts the given array in place and returns it.
static String	join(String[] a, String glue) Joins the array with the given glue to one String.
static Map<Integer,Integer>	loadHistogram(File file) Reads a previously saved histogram from a file.
static int	max(Iterable<Integer> l) Gets the maximal value within the given Iterable.
static int	min(Iterable<Integer> l) Gets the minimal value within the given Iterable.
static void	saveHistogram(Map<Integer,Integer> histo, File file) Writes a histogram to a file.
static void	shuffle(int[] a) Shuffles the content of the given array.
static double	stddev(double[] a) Gets the standard deviation of the array
static int	sum(int[] l) Gets the sum of the values in the array.
static double[]	toDoubleArray(Collection<Double> list) Copies the values of the given collection and unboxes them to an array.
static int[]	toIntArray(Collection<Integer> list) Copies the values of the given collection and unboxes them to an array.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

NumberTools

public NumberTools()

Method Detail

faculty

public static int faculty(int i)

Gets the faculty

Parameters:

i - the number

Returns:

faculty(i)

max

public static int max(Iterable<Integer> l)

Gets the maximal value within the given Iterable.

Parameters:

l - the iterable

Returns:

the maximal number

min

public static int min(Iterable<Integer> l)

Gets the minimal value within the given Iterable.

Parameters:

l - the iterable

Returns:

the minimal number

argMax

public static int argMax(Map<Integer,Integer> l)

Gets the argmax of the given map. The argmax is the key whose value is the maximum within the values.

Parameters:

l - map

Returns:

argmax(map)

sum

public static int sum(int[] l)

Gets the sum of the values in the array.

Parameters:

l - the array

Returns:

sum of the values

cumSum

public static void cumSum(int[] l)

Replaces the values in the given array with the cumulative sum of the array.

Parameters:

l - the array

toIntArray

public static int[] toIntArray(Collection<Integer> list)

Copies the values of the given collection and unboxes them to an array.

Parameters:

list - collection

Returns:

array with the same values

toDoubleArray

public static double[] toDoubleArray(Collection<Double> list)

Copies the values of the given collection and unboxes them to an array.

Parameters:

list - collection

Returns:

array with the same values

createInverse

public static int[] createInverse(int[] a)

Creates the inverse array to the given array. In the inverse array a' of a following condition holds:

a[i] = j ⇔ a'[j] = i

Be careful with sparse arrays, the inverse array could be very large (prefer createInverseAsMap(int[]). It should preferably be used with bijective arrays.

Parameters:

a - the array

Returns:

the inverse

createInverseAsMap

public static Map<Integer,Integer> createInverseAsMap(int[] a)

Creates the inverse map to the given array. In the inverse map a' of a following condition holds:

a[i] = j ⇔ a'.get(j) = i

Parameters:

a - the array

Returns:

the inverse map

createHistogram

public static double[][] createHistogram(Collection<double[]> data,
                                         int numBins,
                                         int... indices)

Creates a histogram from the given data. The returned array matrix contains in the first column the x axis (if the first index of the array matrix denotes the column index) The other columns contain the frequencies of values containing to the corresponding bin of the x axis.

Parameters:

data - data to create the histogram for

numBins - number of bins, the return array matrix will have numBins rows

indices - the indices of the data to create the histogram for

Returns:

histogram

createHistogram

public static int[] createHistogram(int[] a)

Create a histogram for the given array. Be careful with sparse arrays, prefer createHistogramAsMap(int[]).

Parameters:

a - the array to create a histogram for

Returns:

histogram for the array

createHistogramAsMap

public static Map<Integer,Integer> createHistogramAsMap(int[] a)

Create a histogram map for the given array.

Parameters:

a - the array to create a histogram for

Returns:

histogram for the array

saveHistogram

public static void saveHistogram(Map<Integer,Integer> histo,
                                 File file)
                          throws IOException

Writes a histogram to a file. Then it can be loaded by loadHistogram.

Parameters:

histo - the histogram to save

file - the file

Throws:

IOException

loadHistogram

public static Map<Integer,Integer> loadHistogram(File file)
                                          throws IOException

Reads a previously saved histogram from a file.

Parameters:

file - the file

Returns:

the histogram

Throws:

IOException

getHistogramAsString

public static String getHistogramAsString(Map<Integer,Integer> h)

Gets a string representation of the histogram map.

Parameters:

h - histogram

Returns:

string representation

getContentAsBitVector

public static cern.colt.bitvector.BitVector getContentAsBitVector(int[] a)

Gets the content of the given array as BitVector, which means, that the BitVector will have a size equal to the maximal value in the array and contains a 1 for each element which is contained at least once in the array

Parameters:

a - array

Returns:

BitVector for the array

getContentAsArray

public static int[] getContentAsArray(cern.colt.bitvector.BitVector bv)

Gets the indices of the set bits of the given BitVector as array.

Parameters:

bv - the BitVector

Returns:

array with the set indices

shuffle

public static void shuffle(int[] a)

Shuffles the content of the given array.

Parameters:

a - array

convertIntToDouble

public static double[] convertIntToDouble(int[] a)

Performs a deep cast of an int[].

Parameters:

a - the array

Returns:

the casted array

getNumbersTo

public static int[] getNumbersTo(int n)

Gets the numbers from 0 to n in an array.

Parameters:

n - maximal number

Returns:

array of numbers

calculateHistogramDistance

public static double calculateHistogramDistance(Map<Integer,Integer> h1,
                                                Map<Integer,Integer> h2)

Calculates the histogram distance of two histograms.

For reference see Cao & Petzold, Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems, Journal of Computational Physics 212 (2006) 6-24, doi: 10.1016/j.jcp.2005.06.012

Parameters:

h1 - first histogram

h2 - second histogram

Returns:

histogram distance

avg

public static double avg(double[] a)

Gets the avg of the array

Parameters:

a - array

Returns:

avg(array)

stddev

public static double stddev(double[] a)

Gets the standard deviation of the array

Parameters:

a - array

Returns:

stddev(array)

inverse

public static String[] inverse(String[] a)

Inverts the given array in place and returns it.

Parameters:

a - array

Returns:

inverted array

join

public static String join(String[] a,
                          String glue)

Joins the array with the given glue to one String.

Parameters:

a - array

glue - glue

Returns:

joined array

interpolateLinear

public static double[] interpolateLinear(double interval,
                                         double[] time,
                                         double[] value)

Performs a linear interpolation of the values. The array time and the array values must have the same length which means that each element in time is associated with one element in values. The time interval is rescaled to match the given interval and the corresponding values are interpolated.

Parameters:

interval - the interval

time - time array

value - value array

Returns:

interpolated value array

interpolateLinear

public static double interpolateLinear(double desiredTime,
                                       double beforeTime,
                                       double afterTime,
                                       double beforeValue,
                                       double afterValue)

Interpolates a value

Parameters:

desiredTime -

beforeTime -

afterTime -

beforeValue -

afterValue -

Returns:

interpolated value